Ok. When I explicitly mentioned the cavity surften, cavity offset values
based on the paper (amber 12 version) in my input file (amber 22 version),
then non-polar solvation free energy change is decreasing and matching with
the paper. But, total bonding free energy change is zero. How is it
possible ?
While I took the default SASA parameters according to amber22 version, then
total binding free energy change is matching close. Is it because of SASA
parameters in different amber versions (amber 12, amber 22) ya "inp" model
?
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08/28/23,
05:36:07 PM
On Mon, Aug 28, 2023 at 10:43 AM Ray Luo <rluo.uci.edu> wrote:
> No. It's the nonpolar solvent model option.
>
> Ray
>
> On Sun, Aug 27, 2023, 20:25 Kankana Bhattacharjee <
> kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
>
>> Are you talking about internal dielectric constant?
>>
>> On Mon, Aug 28, 2023, 04:43 Ray Luo <rluo.uci.edu> wrote:
>>
>>> The final output shows that you are using the default inp=2 option.
>>> Please set inp=1 in your pb section if you want to seek agreement with the
>>> tutorial setting.
>>>
>>> All the best,
>>> Ray
>>> --
>>> Ray Luo, Ph.D.
>>> Professor of Structural Biology/Biochemistry/Biophysics,
>>> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
>>> Biomedical Engineering, and Materials Science and Engineering
>>> Department of Molecular Biology and Biochemistry
>>> University of California, Irvine, CA 92697-3900
>>>
>>>
>>> On Sun, Aug 27, 2023 at 12:15 PM Kankana Bhattacharjee <
>>> kankana.bhattacharjee_phd21.ashoka.edu.in> wrote:
>>>
>>>> Hello,
>>>>
>>>> I am sharing the "mmpbsa.in
>>>> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
>>>> and "Final-mmpbsa.dat", "energy.dat" files herewith.
>>>>
>>>> Thanks & Regards
>>>> Kankana Bhattacharjee
>>>>
>>>> ---------- Forwarded message ---------
>>>> From: Ray Luo <rluo.uci.edu>
>>>> Date: Sun, Aug 27, 2023 at 11:13 AM
>>>> Subject: Re: [AMBER] MMPBSA-Nonpolar-solvation-energy-parameters:
>>>> To: Kankana Bhattacharjee <kankana.bhattacharjee_phd21.ashoka.edu.in>,
>>>> AMBER Mailing List <amber.ambermd.org>
>>>>
>>>>
>>>> Dear Bhattacharjee,
>>>>
>>>> Can you share your "mmpbsa.in
>>>> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
>>>> and also the result output files?
>>>>
>>>> All the best,
>>>> Ray
>>>>
>>>> All the best,
>>>> Ray
>>>> --
>>>> Ray Luo, Ph.D.
>>>> Professor of Structural Biology/Biochemistry/Biophysics,
>>>> Chemical and Materials Physics, Chemical and Biomolecular Engineering,
>>>> Biomedical Engineering, and Materials Science and Engineering
>>>> Department of Molecular Biology and Biochemistry
>>>> University of California, Irvine, CA 92697-3900
>>>>
>>>> On Fri, Aug 25, 2023 at 12:48 PM Kankana Bhattacharjee via AMBER
>>>> <amber.ambermd.org> wrote:
>>>> >
>>>> > Dear AMBER users,
>>>> >
>>>> > I am trying to reproduce the change in enthalpy of binding of
>>>> > protein-ligand complex using MMPBSA . In the paper, Authors' used
>>>> amber12
>>>> > version and cavity_surften, cavity_offset were set as 0.005420,
>>>> -1.008
>>>> > respectively.
>>>> > Whereas, I am using amber22 version, in this case, default values of
>>>> > cavity_surften, cavity_offset are 0.0378, -0.5692 respectively. When
>>>> my
>>>> > calculations were done using the default (cavity_surften,
>>>> cavity_offset
>>>> > parameters), the result matched closely enough with the paper. But,
>>>> > when I explicitly
>>>> > mentioned the cavity_surften, and cavity_offset parameters (based on
>>>> the
>>>> > paper) in "mmpbsa.in
>>>> <https://urldefense.com/v3/__http://mmpbsa.in__;!!CzAuKJ42GuquVTTmVmPViYEvSg!JxP492qkBoG2rmDufW825f6ZVIrag-hLKZSlKTYwpQF1HlwOqD2e06CgsY6l7oRLFvGs51UaBH4p5FEDkkBTPXM3B75F$>"
>>>> file, I am getting positive enthalpy change of
>>>> > binding !! Could you kindly give suggestions regarding this?
>>>> >
>>>> > Your suggestions would be highly appreciated.
>>>> >
>>>> > Thanks and regards
>>>> > Kankana Bhattacharjee
>>>> > _______________________________________________
>>>> > AMBER mailing list
>>>> > AMBER.ambermd.org
>>>> >
>>>> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!CzAuKJ42GuquVTTmVmPViYEvSg!IMjwHDD5PnwYkCEQW4JOWYqk2BejQdfFCDjMXNKyFtUx5-tN9M6tTMrsJT5DAwvbum7Ea8WHqvM$
>>>>
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>>>> 12:43:33 AM
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>>>
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